Insights from 20 years of bacterial genome sequencing
Since the first two complete bacterial genome sequences were published in 1995, the
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …
Computational methods for strain-level microbial detection in colony and metagenome sequencing data
Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …
Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis
AL Byrd, C Deming, SKB Cassidy… - Science translational …, 2017 - science.org
The heterogeneous course, severity, and treatment responses among patients with atopic
dermatitis (AD; eczema) highlight the complexity of this multifactorial disease. Prior studies …
dermatitis (AD; eczema) highlight the complexity of this multifactorial disease. Prior studies …
Artificial sweeteners induce glucose intolerance by altering the gut microbiota
Non-caloric artificial sweeteners (NAS) are among the most widely used food additives
worldwide, regularly consumed by lean and obese individuals alike. NAS consumption is …
worldwide, regularly consumed by lean and obese individuals alike. NAS consumption is …
Biogeography and individuality shape function in the human skin metagenome
J Oh, AL Byrd, C Deming, S Conlan, HH Kong… - Nature, 2014 - nature.com
The varied topography of human skin offers a unique opportunity to study how the body's
microenvironments influence the functional and taxonomic composition of microbial …
microenvironments influence the functional and taxonomic composition of microbial …
[HTML][HTML] Temporal stability of the human skin microbiome
Biogeography and individuality shape the structural and functional composition of the
human skin microbiome. To explore these factors' contribution to skin microbial community …
human skin microbiome. To explore these factors' contribution to skin microbial community …
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
Metagenomic sequencing increased our understanding of the role of the microbiome in
health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we …
health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we …
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
We present the M etagenomic I ntra-species D iversity A nalysis S ystem (MIDAS), which is
an integrated computational pipeline for quantifying bacterial species abundance and strain …
an integrated computational pipeline for quantifying bacterial species abundance and strain …
Integrated omics endotyping of infants with respiratory syncytial virus bronchiolitis and risk of childhood asthma
Respiratory syncytial virus (RSV) bronchiolitis is not only the leading cause of hospitalization
in US infants, but also a major risk factor for asthma development. While emerging evidence …
in US infants, but also a major risk factor for asthma development. While emerging evidence …